How to detect if a modifier key is pressed when the value of a custom property is changed?
Oki, I eventually found how to get the modifier keys status and how to use the Event structure in a non-modal operator, this thanks to this post:
Python: Ctrl+Click for buttons (capture invocation event)

The answer is pretty straightforward and easy to use once we know it: the invoke function of an operator has an even argument that can easily be queried.

Quick example from the above link:

def invoke(self, context, event):
    wm = context.window_manager

    ev = []
    if event.ctrl:
        ev.append("Ctrl")
    if event.shift:
        ev.append("Shift")
    if event.alt:
        ev.append("Alt")
    if event.oskey:
        ev.append("OS")
    ev.append("Click")

    self.report({'INFO'}, "+".join(ev))

    return wm.invoke_props_dialog(self)